[English] 日本語
Yorodumi
- PDB-2oz3: Crystal structure of L-Rhamnonate dehydratase from Azotobacter vi... -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 2oz3
TitleCrystal structure of L-Rhamnonate dehydratase from Azotobacter vinelandii
ComponentsMandelate racemase/muconate lactonizing enzyme
KeywordsLYASE / ENOLASE / STRUCTURAL GENOMICS / PSI / PROTEIN STRUCTURE INITIATIVE / NEW YORK STRUCTURAL GENOMICS RESEARCH CONSORTIUM / NYSGRC / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


L-rhamnonate dehydratase / L-rhamnonate dehydratase activity / amino acid catabolic process / carbohydrate catabolic process / magnesium ion binding
Similarity search - Function
L-rhamnonate dehydratase / : / Mandelate racemase / muconate lactonizing enzyme family signature 1. / Mandelate racemase/muconate lactonizing enzyme, conserved site / Mandelate racemase/muconate lactonizing enzyme, N-terminal domain / Mandelate racemase / muconate lactonizing enzyme, N-terminal domain / Mandelate racemase/muconate lactonizing enzyme, C-terminal / Mandelate racemase / muconate lactonizing enzyme, C-terminal domain / Enolase C-terminal domain-like / Enolase C-terminal domain-like ...L-rhamnonate dehydratase / : / Mandelate racemase / muconate lactonizing enzyme family signature 1. / Mandelate racemase/muconate lactonizing enzyme, conserved site / Mandelate racemase/muconate lactonizing enzyme, N-terminal domain / Mandelate racemase / muconate lactonizing enzyme, N-terminal domain / Mandelate racemase/muconate lactonizing enzyme, C-terminal / Mandelate racemase / muconate lactonizing enzyme, C-terminal domain / Enolase C-terminal domain-like / Enolase C-terminal domain-like / Enolase-like C-terminal domain / Enolase-like, N-terminal domain / Enolase-like, N-terminal / Enolase-like, C-terminal domain superfamily / Enolase-like; domain 1 / TIM Barrel / Alpha-Beta Barrel / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
L-rhamnonate dehydratase / :
Similarity search - Component
Biological speciesAzotobacter vinelandii AvOP (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsPatskovsky, Y. / Toro, R. / Sauder, J.M. / Freeman, J.C. / Bain, K. / Gheyi, T. / Wu, B. / Wasserman, S.R. / Smith, D. / Gerlt, J. ...Patskovsky, Y. / Toro, R. / Sauder, J.M. / Freeman, J.C. / Bain, K. / Gheyi, T. / Wu, B. / Wasserman, S.R. / Smith, D. / Gerlt, J. / Burley, S.K. / Almo, S.C. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of L-Rhamnonate dehydratase from azotobacter vinelandii
Authors: Patskovsky, Y. / Toro, R. / Sauder, J.M. / Freeman, J.C. / Bain, K. / Wu, B. / Gheyi, T. / Wasserman, S.R. / Smith, D. / Gerlt, J. / Burley, S.K. / Almo, S.C.
History
DepositionFeb 23, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.4Nov 14, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.5Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Aug 30, 2023Group: Advisory / Data collection ...Advisory / Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_unobs_or_zero_occ_atoms / struct_ncs_dom_lim
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id
Revision 1.7Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: Mandelate racemase/muconate lactonizing enzyme
B: Mandelate racemase/muconate lactonizing enzyme
C: Mandelate racemase/muconate lactonizing enzyme
D: Mandelate racemase/muconate lactonizing enzyme
E: Mandelate racemase/muconate lactonizing enzyme
F: Mandelate racemase/muconate lactonizing enzyme
G: Mandelate racemase/muconate lactonizing enzyme
H: Mandelate racemase/muconate lactonizing enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)372,25241
Polymers369,3518
Non-polymers2,90133
Water26,5901476
1
A: Mandelate racemase/muconate lactonizing enzyme
B: Mandelate racemase/muconate lactonizing enzyme
C: Mandelate racemase/muconate lactonizing enzyme
D: Mandelate racemase/muconate lactonizing enzyme
hetero molecules

A: Mandelate racemase/muconate lactonizing enzyme
B: Mandelate racemase/muconate lactonizing enzyme
C: Mandelate racemase/muconate lactonizing enzyme
D: Mandelate racemase/muconate lactonizing enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)373,67958
Polymers369,3518
Non-polymers4,32850
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area53200 Å2
ΔGint-161 kcal/mol
Surface area82610 Å2
MethodPISA, PQS
2
E: Mandelate racemase/muconate lactonizing enzyme
F: Mandelate racemase/muconate lactonizing enzyme
G: Mandelate racemase/muconate lactonizing enzyme
H: Mandelate racemase/muconate lactonizing enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)185,41212
Polymers184,6764
Non-polymers7378
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area44930 Å2
ΔGint-92 kcal/mol
Surface area84500 Å2
MethodPISA
3
E: Mandelate racemase/muconate lactonizing enzyme
F: Mandelate racemase/muconate lactonizing enzyme
G: Mandelate racemase/muconate lactonizing enzyme
H: Mandelate racemase/muconate lactonizing enzyme
hetero molecules

E: Mandelate racemase/muconate lactonizing enzyme
F: Mandelate racemase/muconate lactonizing enzyme
G: Mandelate racemase/muconate lactonizing enzyme
H: Mandelate racemase/muconate lactonizing enzyme
hetero molecules


Theoretical massNumber of molelcules
Total (without water)370,82524
Polymers369,3518
Non-polymers1,47416
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_454-x-1,y,-z-11
MethodPQS
Unit cell
Length a, b, c (Å)170.772, 115.397, 164.113
Angle α, β, γ (deg.)90.00, 96.06, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-3135-

HOH

21D-3088-

HOH

Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A B C D E F G
12A B C D E F G H

NCS domain segments:

Dom-ID: 1 / Refine code: 1

Component-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11ILEILEARGARGAA3 - 155 - 17
21ILEILEARGARGBB3 - 155 - 17
31ILEILEARGARGCC3 - 155 - 17
41ILEILEARGARGDD3 - 155 - 17
51ILEILEARGARGEE3 - 155 - 17
61ILEILEARGARGFF3 - 155 - 17
71ILEILEARGARGGG3 - 155 - 17
12HISHISGLUGLUAA33 - 39535 - 397
22HISHISGLUGLUBB33 - 39535 - 397
32HISHISGLYGLYCC33 - 39635 - 398
42HISHISHISHISDD33 - 39435 - 396
52HISHISGLUGLUEE33 - 39535 - 397
62HISHISGLUGLUFF33 - 39535 - 397
72HISHISHISHISGG33 - 39435 - 396
82HISHISHISHISHH33 - 39435 - 396

NCS ensembles :
ID
1
2

-
Components

#1: Protein
Mandelate racemase/muconate lactonizing enzyme


Mass: 46168.875 Da / Num. of mol.: 8 / Fragment: Residues 238-630
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Azotobacter vinelandii AvOP (bacteria) / Species: Azotobacter vinelandii / Strain: AVOP / Gene: AVIN02004392, AvinDRAFT_6446 / Plasmid: BC-pSGX3(BC) / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: Q4J3N3, UniProt: C1DMY1*PLUS, L-rhamnonate dehydratase
#2: Chemical...
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 31 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1476 / Source method: isolated from a natural source / Formula: H2O

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.25 Å3/Da / Density % sol: 45.46 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 60% Tacsimate, pH 7.0, 10% Glycerol, pH 7.00, VAPOR DIFFUSION, SITTING DROP, temperature 294K

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.9796 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Feb 12, 2006 / Details: MIRRORS
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9796 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 412398 / Num. obs: 412398 / % possible obs: 98.1 % / Observed criterion σ(I): -5 / Redundancy: 2.1 % / Biso Wilson estimate: 31.24 Å2 / Rmerge(I) obs: 0.094 / Rsym value: 0.066 / Net I/σ(I): 3.7
Reflection shellResolution: 2→2.07 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.67 / Mean I/σ(I) obs: 0.6 / Num. unique all: 39577 / Rsym value: 0.56 / % possible all: 94

-
Processing

Software
NameVersionClassification
MOLREPphasing
REFMAC5.3.0028refinement
MAR345CCDdata collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2GSH

2gsh


Resolution: 2→20 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.932 / SU B: 5.962 / SU ML: 0.162 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.213 / ESU R Free: 0.191 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25702 6225 3 %RANDOM
Rwork0.19556 ---
all0.1974 200140 --
obs0.1974 200140 96.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 38.776 Å2
Baniso -1Baniso -2Baniso -3
1--2.05 Å20 Å2-1.28 Å2
2--2.03 Å20 Å2
3----0.25 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms24735 0 188 1476 26399
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02225753
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.1951.95934917
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.86553186
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.20223.0011223
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.231154190
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.41315223
X-RAY DIFFRACTIONr_chiral_restr0.1070.23653
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.0219933
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.140.312442
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2980.516925
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.52799
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.1690.52
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0990.3325
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1840.5138
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it5.3312.515622
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it6.743.525081
X-RAY DIFFRACTIONr_scbond_it9.139410606
X-RAY DIFFRACTIONr_scangle_it11.20169806
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Ens-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A90tight positional0.50.2
1B90tight positional0.390
1C90tight positional0.370
1D90tight positional0.390
1E90tight positional0.380
1F90tight positional0.420
1G90tight positional0.40
2A2776tight positional0.240.2
2B2776tight positional0.250
2C2776tight positional0.40
2D2776tight positional0.280
2E2776tight positional0.350
2F2776tight positional0.280
2G2776tight positional0.30
2H2776tight positional0.320
1A90tight thermal9.835
1B90tight thermal8.580.06
1C90tight thermal5.060
1D90tight thermal12.480
1E90tight thermal6.470
1F90tight thermal6.330
1G90tight thermal7.250
2A2776tight thermal10.455
2B2776tight thermal7.690
2C2776tight thermal8.610
2D2776tight thermal7.620
2E2776tight thermal9.60
2F2776tight thermal5.70
2G2776tight thermal8.270
2H2776tight thermal8.220
LS refinement shellResolution: 2→2.052 Å / Rfactor Rfree error: 0.026 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.389 426 -
Rwork0.301 13309 -
obs-13309 87.97 %

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more